The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences.
The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences.
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DOI：
10.1186/1471-2105-13-s13-s11
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发表时间：
2012
影响因子：
3
通讯作者：
Milosavljevic A
中科院分区：
文献类型：
--
作者：
Riehle K;Coarfa C;Jackson A;Ma J;Tandon A;Paithankar S;Raghuraman S;Mistretta TA;Saulnier D;Raza S;Diaz MA;Shulman R;Aagaard K;Versalovic J;Milosavljevic A
微生物元基因组分析依赖于越来越多的公开可用的工具。这些工具的安装、集成和维护给许多研究人员带来了巨大的负担，并对微生物组分析的采用造成了障碍，特别是在翻译环境中。为了满足这一需求，我们将丰富的微生物组分析工具集成到Genboree微生物组工具集中，并通过Genboree工作台使用软件即服务模式向科学界展示它们。Genboree微生物组工具包为所有生物信息体验级别的用户提供了一个进行微生物组分析的互动环境。该工具集通过提供广泛的分析来驱动假设生成，包括阿尔法多样性和贝塔多样性、系统发育概况、有监督的机器学习和特征选择。我们在两项关于肠道微生物区系的研究中验证了该工具集，一项研究涉及肥胖和瘦弱的双胞胎，另一项研究涉及患有肠易激综合征的儿童。通过降低执行一套全面的微生物组分析的障碍，该工具包使研究人员能够将大量测序数据转化为有价值的生物医学发现。
Microbial metagenomic analyses rely on an increasing number of publicly available tools. Installation, integration, and maintenance of the tools poses significant burden on many researchers and creates a barrier to adoption of microbiome analysis, particularly in translational settings. To address this need we have integrated a rich collection of microbiome analysis tools into the Genboree Microbiome Toolset and exposed them to the scientific community using the Software-as-a-Service model via the Genboree Workbench. The Genboree Microbiome Toolset provides an interactive environment for users at all bioinformatic experience levels in which to conduct microbiome analysis. The Toolset drives hypothesis generation by providing a wide range of analyses including alpha diversity and beta diversity, phylogenetic profiling, supervised machine learning, and feature selection. We validate the Toolset in two studies of the gut microbiota, one involving obese and lean twins, and the other involving children suffering from the irritable bowel syndrome. By lowering the barrier to performing a comprehensive set of microbiome analyses, the Toolset empowers investigators to translate high-volume sequencing data into valuable biomedical discoveries.